[Bioc-devel] MultiAssayExperiment not found in docker devel image

[Nitesh Turaga]

Development work should be done usually on the devel version of Bioconductor (3.12), which is in the bioconductor_docker:devel image.

The stable release, has the latest Bioconductor stable release version 3.11 on the image bioconductor_docker:RELEASE_3_11. 

Hope that answers your question.

Best,

Nitesh 

> On Aug 3, 2020, at 11:46 AM, Joseph Gerrein <gerrein.joseph using gene.com> wrote:
> 
> Hi Nitesh,
> 
> Thank you so much for that detailed explanation! I have just one
> follow-up question – we are internally developing A wrapper for
> MultiAssayExperiment. Do you recommend using the devel version or the
> stable release version?
> 
> Thanks,
> 
> Joe
> 
> On Mon, Aug 3, 2020 at 8:11 AM Nitesh Turaga <nturaga.bioc using gmail.com> wrote:
>> 
>> Hi Joesph,
>> 
>> 1. The RELEASE_3_11 and devel images do not have any installed packages. You are free to install the packages within these images. Please read the help http://bioconductor.org/help/docker/. The goal behind these images is to provide an image where all Bioconductor packages can be installed. Once you install the MultiAssayExperiment package it will load just fine.
>> 
>> 2. The RELEASE_3_11 image is the stable version, the devel version will keep changing every week based on updates in R and any fixes Bioconductor issues.
>> 
>> 3. The bioconductor_docker:bioc2020 image is based on the ‘devel’ image, but a frozen tag during the conference. The docker images used for workshops come with pre-installed packages, and they are derived from the bioconductor/bioconductor_docker:devel image.
>> 
>> I would recommend using the bioconductor/bioconductor_docker:RELEASE_3_11 (stable) image for analysis work. All images provided by Bioconductor are reliable. If you need to report any issues, please use the https://github.com/Bioconductor/bioconductor_docker/issues.
>> 
>> Best,
>> 
>> Nitesh
>> 
>> On Aug 3, 2020, at 11:03 AM, Shepherd, Lori <Lori.Shepherd using RoswellPark.org> wrote:
>> 
>> Marcel or Nitesh?  This was sent to the issue bot.
>> 
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> ________________________________
>> From: Joseph Gerrein <gerrein.joseph using gene.com>
>> Sent: Tuesday, July 28, 2020 11:03 AM
>> To: bioc-issue-bot using bioconductor.org <bioc-issue-bot using bioconductor.org>
>> Cc: Jerry (Zhijun) Tang <jtang using gene.com>; Lala Motlhabi <motlhabl using gene.com>
>> Subject: MultiAssayExperiment not found in docker devel image
>> 
>> Dear bioconductor team,
>> 
>> Hello! I would like to use MultiAssayExperiment in a preloaded bioconductor Docker container that does not require any package installations.  I loaded the docker devel image and also the Docker release 3_11 image (from https://hub.docker.com/r/bioconductor/bioconductor_docker/tags<https://secure-web.cisco.com/1CBV0e1ECW2oH221MZYDrB6ZGZnORfj8i0E9oO6_S0_SuOZu0RxuZrxoZW9vYhbr2tTlHVmXyKmcJ2WgF1J7h4raEyxj58wLe_inCrFX8GSAHS5ffkFppkFmgSUCPTs5LcxpjWSv_mte_V7N06JxxOoJUv5Pud1y9hdtxZESlOdfd1B_VXICfy1Q3I8_82FpVSfJui4CzuCYP49JynqpFLfB01cW6zEwv4Eog3D95hVXysXypD8GZJ4oxWykkGJ-9HtsYnLf01P6EtvTPcNaOur8hADTTJdvz6vJFIi0GES24GSiGjpYgIjRkYOsVcHQPTDx_94vh0mCcsOoa4zQ6EQ/https%3A%2F%2Fhub.docker.com%2Fr%2Fbioconductor%2Fbioconductor_docker%2Ftags>) into Docker desktop on my Windows machine. I wanted to use the MultiAssayExperiment and also SummarizedExperiment, but when I tried to load them using the library function they were not found. Are these docker images preloaded with MultiAssayExperiment?  Do you have any Docker images preloaded with MultiAssayExperiment that are well maintained and/or supported?
>> 
>> I loaded the docker image from the MultiAssayExperiment's/TCGA bioconductor 2020 workshop and I was able to load MultiAssayExperiment using the library function � https://hub.docker.com/r/mr148/multiassayworkshop<https://secure-web.cisco.com/13jSFAuYhSC2URJ4K7zjh4ouo3I63T-6Hw8z5s-Wr2qDEf5SxOaf6kXJP4pWIKe0noQlGgA_GF6LSHHKyxFSt_LM1tgF5_GxjeTCvWXAEtKc2CjiWbaWTzsGBmRYcDqguPf6o52KE_BuYnnGxWJ9_c0WMKjztdEXwZJvZU_cQqn1moo8yPoLpvkf3LXpcDYETRkPKUo6bEpeo3dXxR4sBarXMsI3Rbm9TP30eQM9M2XzFV6-eLG_otc5kS0QZA-wNooTaDtQMDLIouLRkIF1YUHDVDdO9S4MOMaIqNVd-cOLYzpSykcoMr4an7S0DWjLiXoRdO8b1AaEz5PxkLiApiw/https%3A%2F%2Fhub.docker.com%2Fr%2Fmr148%2Fmultiassayworkshop> - Is this container reliable and good to use in general for working with SummarizedExperiment and MultiAssayExperiment in bioconductor?
>> 
>> 
>> Thanks!
>> 
>> Joe
>> 
>> 
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